BMRB Entry 17239

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17239
MolProbity Validation Chart

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Title:
NMR structure of the UBA domain of S. cerevisiae Dcn1 bound to ubiquitin
Deposition date:
2010-10-05
Original release date:
2012-07-25
Authors:
Burschowsky, Daniel; Mattle, Daniel; Rudolf, Fabian; Peter, Matthias; Wider, Gerhard
Citation:

Citation: Burschowsky, Daniel; Rudolf, Fabian; Mattle, Daniel; Peter, Matthias; Wider, Gerhard. "Structural analysis of the ubiquitin-associated domain (UBA) of yeast Dcn1 in complex with ubiquitin (WORKING TITLE)"  .

Assembly members:

Assembly members:
Dcn1-UBA, polymer, 59 residues, 6780.567 Da.
ubiquitin, polymer, 76 residues, 8564.8 Da.

Natural source:

Natural source:   Common Name: baker's yeast   Taxonomy ID: 4932   Superkingdom: Eukaryota   Kingdom: Fungi   Genus/species: Saccharomyces cerevisiae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX-4T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Dcn1-UBA: GSIKRKDASPEQEAIESFTS LTKCDPKVSRKYLQRNHWNI NYALNDYYDKEIGTFTDEV
ubiquitin: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG

Data sets:
Data typeCount
13C chemical shifts201
15N chemical shifts65
1H chemical shifts419

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1UBA1
2ubi2

Entities:

Entity 1, UBA 59 residues - 6780.567 Da.

N-terminal residues number 4 and 5 (GS) are non-native and leftovers from thrombin cleavage

1   GLYSERILELYSARGLYSASPALASERPRO
2   GLUGLNGLUALAILEGLUSERPHETHRSER
3   LEUTHRLYSCYSASPPROLYSVALSERARG
4   LYSTYRLEUGLNARGASNHISTRPASNILE
5   ASNTYRALALEUASNASPTYRTYRASPLYS
6   GLUILEGLYTHRPHETHRASPGLUVAL

Entity 2, ubi 76 residues - 8564.8 Da.

1   METGLNILEPHEVALLYSTHRLEUTHRGLY
2   LYSTHRILETHRLEUGLUVALGLUPROSER
3   ASPTHRILEGLUASNVALLYSALALYSILE
4   GLNASPLYSGLUGLYILEPROPROASPGLN
5   GLNARGLEUILEPHEALAGLYLYSGLNLEU
6   GLUASPGLYARGTHRLEUSERASPTYRASN
7   ILEGLNLYSGLUSERTHRLEUHISLEUVAL
8   LEUARGLEUARGGLYGLY

Samples:

UBA-13C15N+Ub: Dcn1-UBA, [U-80% 13C; U-90% 15N], 0.8 mM; sodium chloride 15 mM; potassium phosphate 110 mM; DTT 2 mM; CHAPS 2 mM; sodium azide 0.02%; sodium chloride 25 mM; ubiquitin 3.2 mM; H2O 95%; D2O 5%

UBA-15N+Ub: Dcn1-UBA, [U-90% 15N], 0.5 mM; sodium phosphate 15 mM; potassium phosphate 110 mM; DTT 2 mM; CHAPS 2 mM; sodium azide 0.02%; sodium chloride 25 mM; ubiquitin 2 mM; H2O 95%; D2O 5%

NMR_Standard_Conditions: ionic strength: 182 mM; pH: 6.15; pressure: 1 atm; temperature: 288 K

Experiments:

NameSampleSample stateSample conditions
3D HCCH-COSYUBA-13C15N+UbisotropicNMR_Standard_Conditions
3D HNCAUBA-13C15N+UbisotropicNMR_Standard_Conditions
3D 1H-13C NOESYUBA-13C15N+UbisotropicNMR_Standard_Conditions
3D 1H-13Caro NOESYUBA-13C15N+UbisotropicNMR_Standard_Conditions
3D 1H-15N TOCSYUBA-15N+UbisotropicNMR_Standard_Conditions
3D HNHBUBA-15N+UbisotropicNMR_Standard_Conditions
3D 1H-15N NOESYUBA-15N+UbisotropicNMR_Standard_Conditions

Software:

UNIO v1.0.4, Herrmann - chemical shift assignment, peak picking

AMBER v9, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

CYANA v2, Guntert, Mumenthaler and Wuthrich - structure solution

TOPSPIN v2.0, Bruker Biospin - processing

CARA v1.8.4, Keller - data analysis

NMR spectrometers:

  • Bruker Avance 700 MHz
  • Bruker Avance 750 MHz
  • Bruker Avance 900 MHz

Related Database Links:

BMRB 17238 11505 11547 15047 15410 15689 15866 15907 16228 16582 16626 16763 16880 16885 16895 17059 17181 17333 17439 17769 17919 18582 18583 18584 18610 18611 18737 19394 19399 19406 19412 19447 25070 25230 4245 4375 4983 5101 5387 6457 6466 6470 6488 68 7111
PDB
DBJ GAA25010 BAA03983 BAA09860 BAA11842 BAA11843 BAA23486
EMBL CAA61706 CAA62639 CAA97697 CAY81363 CAA25706 CAA26488 CAA28495 CAA30183 CAA30815
GB AAB82374 AHY78522 AJP40299 AJV46201 AJV46655 AAA02769 AAA28154 AAA28997 AAA28998 AAA28999
REF NP_013229 NP_001005123 NP_001006688 NP_001009117 NP_001009202 NP_001009286
SP Q12395 P0C273 P0C275 P0C276 P0CG47 P0CG48
TPG DAA09439 DAA18802 DAA20663 DAA20672 DAA24675 DAA28295
PIR I50437 I51568 I65237 JN0790 S13928
PRF 0412265A 1101405A 1212243A 1212243B 1212243C
TPD FAA00319
AlphaFold Q12395 P0C273 P0C275 P0C276 P0CG47 P0CG48

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks